Contacts of the helix formed by residues 392 - 399 (chain D) in PDB entry 3SWD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 392 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ASP* 3.6 24.3 + - + +
3D LYS* 3.7 22.0 - - - +
4D PHE* 3.4 50.5 - - + -
367D ALA* 4.6 0.7 - - - -
389D VAL* 3.3 33.9 - - + +
391D ARG* 1.3 67.9 - - - +
393D TYR* 1.3 60.6 + - - +
394D HIS 2.9 3.6 - - - -
395D ILE* 2.7 32.5 + - + +
396D ASP* 2.9 12.4 + - - +
415D ARG* 3.8 20.9 - - - +
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Residues in contact with TYR 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.7 28.9 - - + -
2D ASP* 5.2 3.9 + - + +
48D LYS* 5.4 1.4 - - - +
391D ARG* 2.9 43.8 + - + +
392D ILE* 1.3 80.4 - - - +
394D HIS* 1.3 99.5 + + - +
396D ASP* 3.3 22.5 + - + +
397D ARG* 3.4 19.0 + - + +
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Residues in contact with HIS 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D ALA* 3.2 31.4 + - + -
368D THR* 3.6 25.8 + - - +
369D ASP 4.3 4.7 - - - +
370D LEU* 3.3 36.1 + - - +
391D ARG* 3.3 20.2 + - + +
393D TYR* 1.3 114.3 + + - +
395D ILE* 1.3 62.2 - - + +
397D ARG* 3.0 28.3 + - - +
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Residues in contact with ILE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 4.8 4.0 - - + -
367D ALA* 4.4 14.8 - - + -
369D ASP 5.0 1.6 - - - +
370D LEU 4.3 7.6 - - - +
373D SER* 3.8 30.3 - - - +
374D ALA* 4.4 3.4 - - + +
377D VAL* 3.5 29.4 - - + -
389D VAL* 4.7 1.8 - - + -
392D ILE* 2.7 28.4 + - + +
394D HIS* 1.3 72.5 - - - +
396D ASP* 1.3 63.2 + - - +
398D GLY* 3.0 2.6 + - - -
399D TYR* 3.0 42.6 + - + +
402D ILE* 4.1 26.7 - - + -
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Residues in contact with ASP 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 5.4 0.3 - - - +
4D PHE* 5.0 2.6 - - - -
47D LEU* 3.4 9.9 - - - +
48D LYS* 3.1 26.2 + - + -
392D ILE* 2.9 19.6 + - - +
393D TYR* 3.7 17.3 - - + +
394D HIS 3.1 0.6 - - - -
395D ILE* 1.3 80.4 - - - +
397D ARG* 1.3 60.3 + - - +
399D TYR 4.0 8.5 - - - +
402D ILE* 5.9 0.9 - - - +
403D GLU* 5.4 0.3 - - - +
415D ARG* 2.5 41.3 + - - -
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Residues in contact with ARG 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 3.7 2.6 - - - -
47D LEU* 3.7 13.1 - - - +
48D LYS* 3.9 22.4 - - + -
49D ASP* 2.9 50.4 + - - +
89D THR 3.9 20.4 + - - -
90D MET* 4.0 10.1 - - - +
115D QPA 2.8 43.6 + - - +
370D LEU* 3.7 26.4 - - + +
393D TYR* 3.4 17.7 + - + +
394D HIS* 3.0 28.1 + - - +
396D ASP* 1.3 78.9 - - - +
398D GLY* 1.3 57.0 + - - +
501D EPZ 4.7 1.4 + - - -
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Residues in contact with GLY 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 3.7 15.9 - - - -
47D LEU* 3.5 12.5 - - - +
231D ASP* 5.1 0.3 - - - +
370D LEU* 3.9 14.8 + - - +
371D ARG* 2.5 28.7 + - - -
394D HIS 3.8 3.2 + - - -
395D ILE 3.0 4.9 + - - -
397D ARG* 1.3 79.6 - - - +
399D TYR* 1.3 63.4 + - - +
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Residues in contact with TYR 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LYS 4.6 0.3 - - - +
47D LEU* 3.8 6.4 - - - +
233D ILE* 4.0 3.0 - - - +
234D GLU* 4.3 29.4 - - + +
237D THR* 3.3 32.7 + - + -
238D PHE* 5.6 0.9 - + - -
309D GLN* 3.6 7.6 + - - -
370D LEU 3.6 21.1 - - - -
371D ARG* 3.3 37.5 + - - -
374D ALA* 3.6 22.5 - - + +
395D ILE* 3.0 26.9 + - + +
396D ASP* 4.0 15.4 - - - +
397D ARG 3.8 0.4 - - - -
398D GLY* 1.3 81.2 - - - +
400D GLU* 1.3 63.4 + - - +
401D ARG 3.3 4.4 + - - -
402D ILE* 4.0 31.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il